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https://github.com/adamtaranto/yanagiba
Filter and slice Nanopore reads which have been basecalled with Albacore.
https://github.com/adamtaranto/yanagiba
Last synced: about 2 months ago
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Filter and slice Nanopore reads which have been basecalled with Albacore.
- Host: GitHub
- URL: https://github.com/adamtaranto/yanagiba
- Owner: Adamtaranto
- License: mit
- Created: 2017-08-04T03:29:18.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-10-11T01:01:25.000Z (about 7 years ago)
- Last Synced: 2024-10-13T20:45:33.054Z (3 months ago)
- Language: Python
- Size: 10.7 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Yanagiba
*A yanagiba is a japanese blade used for cutting sashimi slices. Albacore is a species of tuna. Puns.*
Yanagiba is used to filter short or low quality Oxford Nanopore reads which have been basecalled with
Albacore. Takes fastq.gz and an Albacore summary file as input.
If no Albacore summary file is provided attempt to calculate mean qscore from directly from fastq file
using [NanoMath](https://github.com/wdecoster/nanomath).
*Note:* Calculated quality scores appear to be lower for reads called with Metrichor, you may need to
lower your minqual setting in this case.
# Table of contents
* [Getting started](#getting-started)
* [Installing Yanagiba](#installing-yanagiba)
* [Example usage](#example-usage)
* [Standard options](#standard-options)
* [License](#license)
## Getting started
### Installing Yanagiba
Install from PyPi:
```
pip install yanagiba
```
Clone and install from this repository:
```
git clone [email protected]:Adamtaranto/Yanagiba.git && cd Yanagiba && pip install -e .
```
### Example usage
**Input requirements:**
Albacore summary file must be tab delimited and have the header columns:
- "read_id"
- "sequence_length_template"
- "mean_qscore_template"
Unfiltered reads must be provided as fastq.gz file.
Extract reads from "albacoreReads.fastq.gz" and retain those with a quality score > 10 and
length >= 1000bp. Finally, clip 50 bp from either end of the retained reads and write to
"trimmedreads.fastq.bgz"
```
yanagiba --minlen 1000 --headtrim 50 --tailtrim 50 --minqual 10 \
--summaryfile summary.txt \
--infile albacoreReads.fastq.gz \
--outfile trimmedreads.fastq.bgz
```
*Note:* Output files are in fastq.bgz compressed format. Unzip with:
```
gunzip -c trimmedreads.fastq.bgz > trimmedreads.fastq
```
## Standard options
Run `yanagiba --help` to view the program's most commonly used options:
```
Usage: yanagiba [-h] [-l MINLEN] [-q MINQUAL] [-s SUMMARYFILE] -i INFILE
[-o OUTFILE] [--headtrim HEADTRIM] [--tailtrim TAILTRIM] [-u]
Filter and slice Nanopore reads which have been basecalled with Albacore.
Takes fastq.gz and an Albacore summary file.
Help:
-h, --help Show this help message and exit
Input options:
-i, --infile Input fastq.gz file.
-s, --summaryfile Albacore summary file with header row.
Output options:
-o, --outfile Write filtered reads to this file in .bgz format.
Settings:
-l, --minlen Exclude reads shorter than this length.
(Default: 0)
-q, --minqual Minimum quality score to retain a read.
(Default: 10)
--headtrim Trim x bases from begining of each read.
(Default: 0)
--tailtrim Trim x bases from end of each read.
(Default: None)
-u, --forceunique Enforce unique reads. Only store first instance of a
read from fastq input where readID occurs multiple
times.
(Default: False)
```
## License
Software provided under MIT license.